Integrate finalized manuscript figures and references into the theory documentation

[IvanChernyshov]

Outcome

Synchronize package theory documentation with the final public manuscript after its figures, terminology, and reference list have stabilized.

Scope

• Add or adapt repository-owned figures for:
  • the two-site separator law;
  • three-site cycle compatibility;
  • algebraic fitting versus geometric realization.
• Use editable sources and repository-owned SVG output.
• Add selected foundational references where they improve the theory pages.
• Link the final preprint or publication.
• Synchronize terminology between the manuscript and package theory pages.
• Review captions and surrounding prose for accessibility to graduate-level readers.

Out of scope

• Copying intermediate draft figures.
• Blocking v0.7.
• Importing the manuscript's full numerical-results section into package docs.
• Treating the molecular case study as the package's only use case.

Acceptance criteria

• Figures are based on the final manuscript presentation or are intentionally redrawn for package documentation.
• Sources and generated assets are maintained in the repository.
• The final public manuscript is linked.
• Package and manuscript terminology are consistent.
• Strict docs build passes.

Scheduling

This issue is intentionally unmilestoned and should be revisited after the manuscript reaches its final public form.